Turner 1999
Free Energy Change
Prediction of Stacking
The predicted stacking configuration is the one with lowest free energy change. There are two possible configurations.
Configuration 1:
Helix 1 with 5' dangling U, Helix 2 with 3' dangling C, and Helix 3 with a GG mismatch
∆G°37 = ∆G°37(AU with 5' dangling U) + ∆G°37(CG with 3' dangling C) + ∆G°37(CG with GG mismatch)
∆G°37 = –0.2 kcal/mol – 0.8 kcal/mol – 1.6 kcal/mol
∆G°37 = –2.6 kcal/mol
Configuration 2:
Helix 1 in a flush coaxial stack with Helix 2 and Helix 3 with a GG mismatch
∆G°37 = ∆G°37(coaxial stack of AU followed by GC) + ∆G°37(CG with GG mismatch)
∆G°37 = –2.08 kcal/mol – 1.6 kcal/mol
∆G°37 = –3.7 kcal/mol
Therefore, configuration 2, -3.7 kcal/mol, is the predicted free energy change.